Variant report

Variant	rs200371
Chromosome Location	chr20:22269440-22269441
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs169228	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199782	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199783	0.86[ASN][1000 genomes]
rs199792	0.85[ASN][1000 genomes]
rs200359	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs200364	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200365	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs200367	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs200370	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383250	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs427808	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804687	0.83[ASN][1000 genomes]
rs804691	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs804692	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804693	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804699	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058137	chr20:21549350-22295051	Weak transcription Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv962639	chr20:22254826-22283685	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs200371	NXT1	cis	parietal	SCAN
rs200371	CST9L	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22268800-22269800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:22268800-22270000	Enhancers	Fetal Muscle Leg	muscle
3	chr20:22268800-22270400	Enhancers	HMEC	breast
4	chr20:22268800-22270400	Enhancers	HSMM	muscle
5	chr20:22268800-22271000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:22268800-22271000	Enhancers	NHEK	skin
7	chr20:22268800-22271400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:22269000-22270000	Enhancers	HSMMtube	muscle
9	chr20:22269200-22270200	Enhancers	Muscle Satellite Cultured Cells	--

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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